All good points for a larger project,
yet less interesting for a personal cluster when the budget is small
and the personal desktop and personal work environment is Ubuntu. I do
suspect that in 18 months or so the original poster will be looking to
update his environment and your good summary will then be apropos.
Especially the bit "a source based "ports-like" tree for building scientific
packages, and then we integrate with Environment Modules to make them
available for the users.....". See module-assistant in Ubuntu and friends.
I just deleted a longish comparison of GenToo and British sports cars. Since
the OP is not a mechanic and does not have a staff, mechanic or chauffeur to
maintain his roadster. I suspect he needs a Toyota, Ford or Chevy with an
automatic transmission that he can maintain himself (for now).
Oh wait I almost retyped it all.... ;-)
On Mon, Oct 12, 2009 at 11:50:10AM -0700, Greg Kurtzer wrote:
> On Sun, Oct 11, 2009 at 1:29 PM, Nifty Tom Mitchell
> <niftyompi at niftyegg.com> wrote:
> > On Mon, Oct 05, 2009 at 12:02:11PM +0200, Tomislav Maric wrote:
> >> Nifty Tom Mitchell wrote:
> >> > On Sun, Oct 04, 2009 at 01:08:27PM +0200, Tomislav Maric wrote:
> >> >> Mark Hahn wrote:
> >> >>>> I've seen Centos mentioned a lot in connection to HPC, am I making a
> >> >>>> mistake with Ubuntu??
> >> >>> distros differ mainly in their desktop decoration. for actually
> >> >>> getting cluster-type work done, the distro is as close to irrelevant
> >> >>> as imaginable. a matter of taste, really. it's not as if the distros
> >> >>> provide the critical components - they merely repackage the kernel,
> >> >>> libraries, middleware, utilities. wiring yourself to a distro does
> >> >>> affect when you can or have to upgrade your system, though.
> >> >>>
>> I seem to not have the original sources to this thread, but this is
> something that I thought I should chime in on.
>> The underlying components that make up a distribution are in-fact an
> important component to an HPC system in its entirety. There are many
> reasons for this, but I will focus on just a few that I hope don't
> strike too much of a religious chord with people while at the same
> time letting me rant a bit. ;-)
>>>> 1) HPC people are quite familiar with building their scientific apps
> with optimized compilers and libraries. If an application is linking
> against any OS libraries (yes, including the C library) it would
> probably make sense to make sure those have been compiled with an
> optimal build environment. Most distributions do not do this, as for a
> single standalone system the results may or not even be noticeable. I
> have been part of large benchmark projects to evaluate the differences
> of the distributions. In a nutshell, differences become more obvious
> at scale.
>> 2) Distributions focused on non-HPC targets may not include tools,
> libraries or even functions that would be beneficial for HPC. And in
> addition to that, they may not be included in a way that makes it very
> usable. For example, Just because a distribution contains a package
> does not mean that is what people should use. For example, using a
> distribution supplied version of Open MPI would be an injustice to the
> majority of cluster users, but many distributions consider themselves
> HPC ready because they have some HPC capable libs.
>> It is more important to have a solution for creating a suitable HPC
> environment. For example, in Caos NSA the core OS is RPM based but we
> also utilize a source based "ports-like" tree for building scientific
> packages, and then we integrate with Environment Modules to make them
> available for the users. So one can do:
>> # cd /usr/src/cports/packages/openmpi/1.3.3
> # make install COMPILERS=intel
> # make clean
> # make install COMPILERS=gcc
> # su - user
> $ module load openmpi/1.3.3-intel
> $ mpicc -show
> icc ........
> $ module unload openmpi
> $ module load openmpi/1.3.3-gcc
> $ mpicc -show
> gcc ........
>>> 3) HPC distributions should be focused on being lightweight and
> efficient. Bloat free stateless environments are important for keeping
> node operating systems quiet and supportive of HPC code. Lightweight
> and bloat free does not mean an ancient and featureless core
> environment either.
>> 4) Even the kernel for most distributions is tuned for desktop use
> which tries to give the fairest share of CPU time to all processes
> (obviously not HPC supportive).
>> 5) Clusters are not worth BETA quality code. Unstable environments
> with no long term plans for upstream support makes it a ridiculous
> solution for anybody trying to build a production environment. The
> number of unsuitable solutions that we had to "rescue" because they
> were running Fedora and totally unmaintainable by the people that
> integrated them is just silly.
>>> It really is a shame that religion plays such a big part of what OS
> someone would use because each OS (even non-Linux) are good for
> certain things. I can understand wanting to leverage an economy of
> scale with a homogenous environment, but there is a particular point
> where the economy of scale is no longer justified when shoe-horning a
> non-suitable solution onto a cluster. Where that line is really
> depends on the admins, users, the size of the system, and what they
> baseline their benchmark for success at.
>> Just my $0.02 for what it's worth.
>> Greg
>>> --
> Greg M. Kurtzer
> Chief Technology Officer
> HPC Systems Architect
> Infiscale, Inc. - http://www.infiscale.com
--
T o m M i t c h e l l
Found me a new hat, now what?
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